NovaSeq X plus and ATACseq data

[leqi0001]

Hi,

I'm debating whether I should use NovaSeq X plus for my ATACseq libraries. I've tried this previously, which gave me much much lower % of mononucleosomal fragments compared to NovaSeq 6000. I think this is expected given its stronger bias to smaller fragments. How strong an effect would you expect from this type of shifted fragment length in terms of peak calling and differential accessibility analysis?

Thanks!

[torpedosmirk]

Hi,

I'm debating whether I should use NovaSeq X plus for my ATACseq libraries. I've tried this previously, which gave me much much lower % of mononucleosomal fragments compared to NovaSeq 6000. I think this google baseball is expected given its stronger bias to smaller fragments. How strong an effect would you expect from this type of shifted fragment length in terms of peak calling and differential accessibility analysis?

Thanks!

When using the NovaSeq X Plus for ATAC-seq libraries, you may encounter some issues with peak calling and differential accessibility analysis. In fact, the lower proportion of single nucleosome fragments may result in fewer peaks being detected, as many peak calling algorithms are optimized for specific nucleosome models. This may result in weak peak signals, leading to under-detection or omission of important regulatory regions. As a result, regions with differential accessibility between samples may be underestimated, which may lead to misunderstandings about gene regulation.